Glossary of Terms

This glossary of terms is shared among all Lasergene applications. Many terms may not apply to the application whose help you are currently viewing.

Term	Definition
ab1	File extension for an Invitrogen Corporation (formerly PE Applied Biosystems, Inc.) automated sequencer trace file.
abi	File extension for an Invitrogen Corporation (formerly PE Applied Biosystems, Inc.) automated sequencer trace file.
ace	File extension for a Phrap assembly document.
Alignment view	(SeqMan) The Alignment View displays the consensus sequence and the alignment of all sequences making up a contig and is where editing occurs.
Alpha	One of the four protein classes in the Secondary Structure – Chou-Fasman methods. Representatives of the Alpha class are composed primarily of α-helices with little ß-sheet structures. Hemoglobins and cytochromes are typical Alpha class proteins.
Alpha plus beta	One of the four protein classes in the Secondary Structure – Chou-Fasman methods. Alpha plus Beta contains both α-helix and ß-sheet structures, with separate domains. Ferrodoxins and ribonucleases are typical of this class.
Alpha/Beta	One of the four protein classes in the Secondary Structure – Chou-Fasman methods. The Alpha/Beta class contains proteins with alternating α and ß character and mixed domains. Representatives of the Alpha/Beta class include dehydrogenases and kinases.
ari	Extension for an Ariadne pattern descriptor file.
Assay surface	(GeneQuest) Portion of the assay document where method results are graphically displayed.
Beta	One of the four protein classes in the Secondary Structure – Chou-Fasman methods. Beta class contains ß-sheet proteins, with little or no α-helix character. Examples include immunoglobulins and serine proteases.
BLAST	A tool for searching protein or DNA sequence against other sequences stored in a BLAST (Basic Local Alignment Search Tool) database.
Chromatogram	Trace data from a fluorescent sequencing instrument.
Constituent sequences	DNA sequence fragments used to assemble finished contiguous sequences.
Contig	Contiguous DNA sequence; a consensus sequence from an assembly project.
Contig scaffold	A collection of contigs having a member of one or more pairs of reads in common. Contig scaffolds are created automatically by choosing Order Contigs but may also be created manually using the Create New Scaffold command.
Contig info	The Contig Info window provides a statistical summary report for a selected contig.
ct	File extension for an RNA picture saved as a ConnecT file.
dad	File extension for a GeneQuest DNA Assay Document.
dao	File extension for a GeneQuest DNA Assay Outline.
dat	File extension that identifies a GeneQuest transcription factor file.
Default method outline	(GeneQuest) The Method Outline that is automatically applied to all new assay documents. The outline contains information about which methods to place in the method curtain and which of those to apply to the assay surface.
Delta-G (∆-G)	Free energy.
dnd	File extension for a Phylip file.
Dual-end	Dual-end sequence data are forward and reverse sequence reads originating at opposite ends of the same fragment.
eff	File extension for an extended file of filenames, a binary format file of filenames that also contains optimized assembly order information.
embi	File extension for a text-based sequence file in the format specified by the European Molecular Biology Laboratory.
Entrez	A database of DNA and protein sequences and annotations that may be searched using Boolean text queries. Entrez servers may be accessed via the Internet or, if available, your Intranet. Lasergene's default Internet Entrez server points to the National Center for Biotechnology Information (NCBI). Detailed information about NCBI's Entrez database is available at https://www.ncbi.nlm.nih.gov/books/NBK25500.
EST	Expressed Sequence Tag.
exe	File extension that identifies a program (EXEcutable) file.
Extended FastA	Extended FastA is a file format containing the sequence name and the sequence, as well as information about the path for the file, trim information, and its layout position in the assembly.
Extended file of filenames (eff)	(SeqMan) A binary format file of filenames that also contains optimized assembly order information. These files use .eff as a file extension.
ezd	File extension that identifies restriction enzyme library used in SeqBuilder Pro and GeneQuest.
FastA	A FastA formatted sequence begins with a single-line description, followed by lines of sequence data of about 80 characters or less in length. The description line is distinguished from the sequence data by typing a greater-than (">") symbol prior to beginning the description.
File of filenames (FOF)	(SeqMan) A file of filenames (FoF) is used to make multiple sequence files more convenient for SeqMan to access at once. You can trim, scan for vector, and screen for contaminants, then save this information in the FoF. You can then assemble it many times without having to redo the trimming and scanning. Also, .fof is the file extension for a file of filenames.
gbk	File extension for a text-based sequence file in GenBank format, as specified by the National Center for Biotechnology Information.
GCG	Genetics Computer Group®.
Genefont	A fixed-space Lasergene font useful for maintaining spacing of sequence data.
GeneQuest	Lasergene module for locating potential genes and other features of interest in DNA sequences.
GenVision	DNASTAR’s visualization tool for genomic data. For more information, see the GenVision product page on the DNASTAR website.
IUB codes	International Union of Biochemistry standard genetic codes.
K-tuple	A user defined number (k) of adjacent residues that form an exact match in both sequences.
Legend Curtain	(GeneQuest) Area which stores labels for each method on the assay surface. See Using the Method and Legend Curtains for more information.
lyt	File extension for a SeqBuilder Pro layout file.
MapDraw	Lasergene module for multiple and pairwise sequence alignments and phylogenetic tree creation.
mat	File extension for a Borodovsky MATrix file.
mer	Unit of length for a DNA sequence fragment. For example, a hexamer (6-mer) is a DNA fragment six base pairs long.
Method Curtain	(GeneQuest) Area which stores analysis and annotation methods for possible inclusion in the assay. See Using the Method and Legend Curtains for more information.
Method outline	(GeneQuest) A file containing directions specifying which methods should appear in the method curtain and which of those should be applied to the assay surface. Any associated parameters or display options (color, line weight, etc.) are recorded as part of the outline.
mpd	File extension for a MapDraw document.
msf	Extension for a Multiple Sequence Format project file, native to GCG's Pileup program.
nex	Extension for the PAUP Nexus phylogeny file format (version 4.0).
Object selector	(GeneQuest) The hand-shaped palette tool on the left of the assay document. It is used to select and manipulate entire method displays.
ORF	Open Reading Frame.
pad	Extension for a Lasergene Protein Assay Document.
Palindrome	Any text (e.g., sequence text) reading the same in both directions; "racecar," for example.
PAM	Point Accepted Mutations. One PAM represents one mutation per 100 residues (e.g., PAM250 means 2.5 mutations per residue).
pao	Extension for a Lasergene Protein Assay method Outline.
pau	Extension for the PAUP Nexus phylogeny file format (version 3.0).
PAUP	Phylogenetic Analysis Under Parsimony.
phd	Extension for a trace file re-called by Phred.
pms	Extension for a Lasergene primer conditions file.
pri	Extension for an auxiliary primer catalog.
Project Statistics	(SeqMan) The Project Statistics Window summarizes information for every contig in a project, including contig length, total sequence length, and the number of sequences in the contig (total, top strand and bottom strand).
Project Summary	(SeqMan) The Project Summary window lists the assembled contigs in the upper pane and the constituent sequences for all contigs in the lower pane.
Prosite	Prosite (http://www.expasy.ch/prosite) contains biologically significant motifs, patterns, sites and complete annotation fields, derived by analyzing primary sequence, structural and functional data of groups of proteins. It is used to elucidate function and to determine protein family membership in uncharacterized proteins.
Range selector	(GeneQuest) The arrow-shaped palette tool on the left of the assay document. It is used to select a range within the protein sequence.
Report window	(SeqMan) The Report window summarizes such things as assembly time and the parameters used in constructing a contig.
rtc	File extension for a genetic codes file.
sbd	File extension for files created and saved using the Lasergene module, SeqBuilder Pro.
Scaffold Strategy View	(SeqMan) The Scaffold Strategy View graphically summarizes the position and orientation of every constituent sequence in a scaffold of contigs.
scf	File extension for a sequence file saved in Standard Chromatogram Format.
seq	Extension for a Lasergene DNA SEQuence file.
SeqBuilder Pro	Lasergene module for editing nucleic and amino acid sequences. Also used to view sequences in a variety of ways.
SeqMan	Lasergene module for assembling individual sequence fragments into a finished DNA sequence.
Sequencher	A fragment assembly and sequencing project management tool produced by GeneCode Corp. Sequencher is a trademark of GeneCodes Corp.
Set Ends	Clicking the Set Ends button in the New or Open dialogs allows you to specify a nucleotide sequence subrange, or to choose the complement of the sequence.
sff	File extension for a Standard Flowgram Format file, which contains sequence trace data generated using 454 technology.
sqd	File extension for a DNASTAR SeqMan assembly project.
Start codon	The AUG codon of a transcript used to encode the first amino acid of the corresponding protein.
Stop codon	A codon (UAA, UAG or UGA in the Standard Genetic Code) that signals the termination of translation.
Strategy View	(SeqMan) The Strategy View graphically summarizes the position and orientation of every constituent sequence in a contig.
Tm	Melting Temperature.
Trace data	DNA sequence data from a fluorescent sequencing instrument (also called Chromatograms).
Trace/Flowgram Data View	(SeqMan) A window showing a graphic display of a sequence chromatogram or flowgram, accessed via Sequence>Show Original Trace/Flowgram Data.
Unassembled Sequences Window	(SeqMan) The Unassembled Sequences Window opens automatically upon initiation of SeqMan, and later displays input sequences available for assembly.
Unlocated contigs	The default scaffold in which contigs appear unless placed in scaffolds using the Create New Scaffold or Order Contig commands.
vct	File extension for a Lasergene vector file.
wmf	Extension for the Windows Meta File graphic file format.